oh, I didn't give my answer to your question.
I would say which one's harder between Junior and DK3 is kinda apples and oranges.
Games that give you a fixed number of lives are hard in a different way than games that give you lives at a steady drip.
"Limited lives" games are primarily a matter of staying focused and not screwing up. Games with a lot of random elements (like DK, and the chain board on Junior) add screwings and/or "much harder than they usually are" boards to the mix. Skill is actually secondary to focus in games like this. This is why you will have the raw skill/knowledge to get "x" score in DK a long time before you actually get the score (and one of the reasons why the game kinda turns me off nowadays). I'm *capable* of getting a million points, but is my brain going to be able to NOT shit its pants at least a few times over the course of two and a half hours of play? Not usually. So it's incredibly tedious to grind for scores on games like this. One distracting thought, one hand-slipped-off-the-joystick, one ridiculously hard board, and one [whatever else], and that's it. Game over, because you only get 4 chances in the 2-3 hours you'll be playing.
"Steady extras" games, though, are different, because they are more about pure skill. All you have to do is get good enough at the game to collect extra lives at a rate faster than the rate at which you lose them. Once you're at that point, you'll probably get the score that you're capable of in most of your runs. This is the beauty of that type of game, and why I've come to enjoy them more. If you make a momentary mistake or two or three, you can recover in a way that you can't in limited-lives games. If I die on the 10th board in DK3 or Robotron, it doesn't matter. If I die on the 10th board of DK or Junior, oh well, time to restart and slog through that boring grind again.
So I think DK3 1M requires the acquisition of a lot more skill, muscle memory, and reflex than DK Junior 1M, which is much more about simply learning and applying patterns. The difficulty on Junior is applying them perfectly for 80-odd boards in sequence, which is gonna come down more to how sharp your brain is that day.